Omics - Analysis of large-scale biomolecular datasets

Introduction to Linux

Course date: 04 November 2025

Last modified: 2025-10-29

Welcome to Linux Commands! 🐧

This presentation will teach you the fundamental Linux commands you’ll need to navigate and work with the command line.

What we’ll cover:

• Navigation commands (pwd, ls, cd, paths)
• File operations (mkdir, touch, cp, mv, rm, tar)
• Text processing (cat, grep, less, head, tail, nano)
• System information (whoami, uname, df, top)
• Package management
• Getting help and shortcuts

Getting Started

Opening the Terminal

• macOS: Press Cmd + Space, type “Terminal”, press Enter
• Linux: Press Ctrl + Alt + T
• Windows: Use WSL or Git Bash

Your First Command

#| eval: true
# This is a comment - it won't execute
echo "Hello, Linux!"

Try running this command in your terminal!

exit - Exit the Terminal

Closes the current shell session.

exit

Navigation Commands

pwd - Print Working Directory

Shows your current location in the file system.

pwd

ls - List Directory Contents

Lists files and directories in the current directory.

ls
ls -l  # Long listing format
ls -a  # Show hidden files

cd - Change Directory

Changes your current working directory.

cd directory_name  # Relative path
cd /absolute/path  # Absolute path
cd ..              # Go up one directory
cd ~               # Go to home directory
cd -               # Go to previous directory

Absolute vs Relative Paths

• Absolute paths: Start with / and specify the full path from root
• Relative paths: Start from current directory, use . for current, .. for parent

# Absolute path
cd /home/user/documents

# Relative path
cd documents  # If you're in /home/user/
cd ../sibling # Go to sibling directory

File Operations

mkdir - Make Directory

Creates a new directory.

mkdir my_folder                    # Create single directory
mkdir -p parent/child/grandchild   # Create nested directories

touch - Create Empty File

touch new_file.txt                   # Create single empty file
touch file1.txt file2.txt file3.txt  # Create multiple files

cp - Copy Files

cp source.txt destination.txt        # Copy single file
cp -r source_dir destination_dir     # Copy directory recursively

More File Operations

mv - Move/Rename Files

mv old_name.txt new_name.txt     # Rename
mv file.txt /path/to/directory/  # Move

rm - Remove Files

rm file.txt
rm -r directory/
rm -i file.txt      # Interactive mode

⚠️ Warning: rm -rf / will delete everything! Be careful!

tar - Archive Files

Create and extract compressed archives.

# Create archive
tar -czf archive.tar.gz directory/

# Extract archive
tar -xzvf archive.tar.gz

# List archive contents
tar -tzf archive.tar.gz

Text Processing

cat - Concatenate and Display

cat file.txt              # Display single file
cat file1.txt file2.txt   # Display multiple files

grep - Search Text

grep "search_term" file.txt          # Search in single file
grep -r "pattern" /path/to/search/   # Search recursively
grep -i "case_insensitive" file.txt  # Case-insensitive search

less - View File Contents

Views file contents one page at a time (better than cat for large files).

less file.txt
# Navigation: space (next page), b (previous), q (quit)

head - Show Beginning of File

Shows the first few lines of a file.

head file.txt
head -n 20 file.txt  # First 20 lines

tail - Show End of File

Shows the last few lines of a file.

tail file.txt
tail -n 20 file.txt  # Last 20 lines
tail -f file.txt     # Follow file (real-time updates)

nano - Simple Text Editor

Basic command-line text editor.

nano file.txt
# Ctrl+O (save), Ctrl+X (exit), Ctrl+W (search)

System Information

whoami - Who Am I?

whoami

uname - System Information

uname -a  # Show all system information
uname -r  # Show kernel release version

df - Disk Free Space

df -h  # Show disk usage in human-readable format

top - Monitor Processes

Shows real-time system processes and resource usage.

top  # Display running processes with CPU/memory usage
# Press 'q' to quit, 'h' for help

Package Management

Ubuntu/Debian (apt)

sudo apt update
sudo apt install package_name
sudo apt remove package_name

CentOS/RHEL (yum/dnf)

sudo yum install package_name
sudo yum remove package_name

macOS (brew)

brew install package_name
brew uninstall package_name

Useful Shortcuts

Command Line Shortcuts

• ↑/↓ - Navigate command history
• Tab - Auto-complete commands/files
• Ctrl + C - Cancel current command
• Ctrl + L - Clear screen
• Ctrl + A - Go to beginning of line
• Ctrl + E - Go to end of line

Wildcards

Wildcards are special characters that allow you to match multiple files or directories based on patterns, making it easier to work with groups of files.

• * - Matches any characters
• ? - Matches single character
• [abc] - Matches any of a, b, or c

Example:

ls *.txt              # List all files ending with .txt
cp file?.txt backup/  # Copy files like file1.txt, file2.txt to backup/

ls linux_practice/*.txt  # List all .txt files in linux_practice

Getting Help

man - Manual Pages

man ls
man -k "search term"

–help Flag

ls --help

tldr - Simplified Help

tldr ls

Common Mistakes & Tips

Common Errors

• Permission denied - Use sudo for admin tasks
• Command not found - Check spelling, PATH
• No such file or directory - Verify paths

Best Practices

• Use ls before rm to double-check
• Use man or --help for unfamiliar commands
• Backup important files before operations
• Use tab completion to avoid typos

Next Steps

What to Learn Next

• File permissions (chmod, chown)
• Process management (ps, kill)
• Advanced text editors (vim, emacs)
• Shell scripting basics
• Networking commands (ping, curl, ssh)
• User management (useradd, passwd)

Resources

• Linux Command Line Basics
• ExplainShell - Explains shell commands
• tldr - Simplified command documentation

Quiz Time! 🧠

Question 1

Which command shows your current directory? - A) ls - B) pwd - C) cd

Question 2

How do you create a new directory? - A) touch newdir - B) mkdir newdir - C) cp newdir

Question 3

What’s the safest way to delete a file? - A) rm file.txt - B) rm -rf file.txt - C) rm -i file.txt

(Answers: 1-B, 2-B, 3-C)

Thank You!

You’ve completed the basic Linux commands tutorial!

Remember:

• Practice regularly
• Use man for help
• Start with simple commands
• Build complexity gradually

Questions?

Feel free to ask your instructor or classmates!

🐧 Happy Linux learning! 🐧

Practice Time! 💻

Exercise 1: Navigation

1. Open your terminal
2. Check your current directory with pwd
3. List the contents with ls
4. Create a new directory called linux_practice
5. Change into that directory

pwd
ls -la
mkdir -p linux_practice
cd linux_practice

Exercise 2: File Operations

1. Create a text file called notes.txt
2. Add some text to it using echo "Hello Linux" > notes.txt
3. Display the contents with cat
4. Copy the file to backup.txt
5. List the directory contents

echo "Hello Linux" > notes.txt
cat notes.txt
cp notes.txt backup.txt
ls -la